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Toolbox for Complex Networks and Graphs

Is there a toolbox which helps in visual simulation and modeling of a network (say a mesh or ring) consisting of coupled synchronized system of nonlinear equations(ODE) which represent a system of ...
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Does the spin glass corresponding to a restricted Boltzmann machine have a characteristic timescale?

From what I gather, a Boltzmann machine can be identified with a spin glass. Though I don't know the details yet (and would welcome any references within the last 5 years--not, e.g. MacKay, etc.), I ...
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Degree-degree correlations in networks

In their paper Specificity and Stability in Topology of Protein Networks (Science 2002) Maslov and Sneppen introduced a null-model to evaluate degree-degree correlations in networks. Maslov also ...